LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.61496 3.61496 3.61496 Created orthogonal box = (0 -38.9379 0) to (19.4671 38.9379 3.61496) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.69897 4.69897 3.61496 Created 234 atoms create_atoms CPU = 0.000202179 secs 234 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.69897 4.69897 3.61496 Created 234 atoms create_atoms CPU = 8.2016e-05 secs 234 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.71575 ghost atom cutoff = 7.71575 binsize = 3.85788, bins = 6 21 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.71575 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 456 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.71575 ghost atom cutoff = 7.71575 binsize = 3.85788, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.71575 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.49 | 4.49 | 4.49 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1602.2958 0 -1602.2958 -5421.6683 19 0 -1606.5254 0 -1606.5254 -10764.195 Loop time of 0.061554 on 1 procs for 19 steps with 456 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1602.29577609 -1606.52378819 -1606.5253576 Force two-norm initial, final = 6.74137 0.101152 Force max component initial, final = 2.50158 0.0110838 Final line search alpha, max atom move = 1 0.0110838 Iterations, force evaluations = 19 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060274 | 0.060274 | 0.060274 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083327 | 0.00083327 | 0.00083327 | 0.0 | 1.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000447 | | | 0.73 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4359 ave 4359 max 4359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78376 ave 78376 max 78376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78376 Ave neighs/atom = 171.877 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -1606.5254 0 -1606.5254 -10764.195 5480.3517 25 0 -1606.6556 0 -1606.6556 -1049.4986 5442.0545 Loop time of 0.0109742 on 1 procs for 6 steps with 456 atoms 91.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1606.5253576 -1606.65543284 -1606.65561751 Force two-norm initial, final = 50.4381 1.12551 Force max component initial, final = 37.9473 1.10646 Final line search alpha, max atom move = 0.000738066 0.00081664 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010354 | 0.010354 | 0.010354 | 0.0 | 94.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015736 | 0.00015736 | 0.00015736 | 0.0 | 1.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004628 | | | 4.22 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4439 ave 4439 max 4439 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76616 ave 76616 max 76616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76616 Ave neighs/atom = 168.018 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.71575 ghost atom cutoff = 7.71575 binsize = 3.85788, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.71575 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1606.6556 0 -1606.6556 -1049.4986 Loop time of 9.53674e-07 on 1 procs for 0 steps with 456 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4479 ave 4479 max 4479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77044 ave 77044 max 77044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77044 Ave neighs/atom = 168.956 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.629 | 4.629 | 4.629 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1606.6556 -1606.6556 19.432191 77.875829 3.5961552 -1049.4986 -1049.4986 325.16394 -3508.1093 34.449451 2.3370538 283.95729 Loop time of 1.90735e-06 on 1 procs for 0 steps with 456 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.907e-06 | | |100.00 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4479 ave 4479 max 4479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38522 ave 38522 max 38522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77044 ave 77044 max 77044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77044 Ave neighs/atom = 168.956 Neighbor list builds = 0 Dangerous builds = 0 456 -1606.65561751148 eV 2.33705378710357 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00